NMR of conotoxins: structural features and an analysis of chemical shifts of post-translationally modified amino acids

Conotoxins are small conformationally constrained peptides found in the venom of marine snails of the genus Conus. They are usually cysteine rich and frequently contain a high degree of post-translational modifications such as C-terminal amidation, hydroxylation, carboxylation, bromination, epimerisation and glycosylation. Here we review the role of NMR in determining the three-dimensional structures of conotoxins and also provide a compilation and analysis of H-1 and C-13 chemical shifts of post-translationally modified amino acids and compare them with data from common amino acids. This analysis provides a reference source for chemical shifts of post-translationally modified amino acids. Copyright (C) 2006 John Wiley & Sons, Ltd.

Adiponectin multimerization is dependent on conserved lysines in the collagenous domain: Evidence for regulation of multimerization by alterations in posttranslational modifications

Adiponectin is a secreted, multimeric protein with insulin-sensitizing, antiatherogenic, and antiinflammatory properties. Serum adiponectin consists of trimer, hexamer, and larger high-molecular-weight (HMW) multimers, and these HMW multimers appear to be the more bioactive forms. Multimer composition of adiponectin appears to be regulated; however, the molecular mechanisms involved are unknown. We hypothesize that regulation of adiponectin multimerization and secretion occurs via changes in posttranslational modifications (PTMs). Although a structural role for intertrimer disulfide bonds in the formation of hexamers and HMW multimers is established, the role of other PTMs is unknown. PTMs identified in murine and bovine adiponectin include hydroxylation of multiple conserved proline and lysine residues and glycosylation of hydroxylysines. By mass spectrometry, we confirmed the presence of these PTMs in human adiponectin and identified three additional hydroxylations on Pro71, Pro76, and Pro95. We also investigated the role of the five modified lysines in multimer formation and secretion of recombinant human adiponectin expressed in mammalian cell lines. Mutation of modified lysines in the collagenous domain prevented formation of HMW multimers, whereas a pharmacological inhibitor of prolyl- and lysyl-hydroxylases, 2,2'-dipyridyl, inhibited formation of hexamers and HMW multimers. Bacterially expressed human adiponectin displayed a complete lack of differentially modified isoforms and failed to form bona fide trimers and larger multimers. Finally, glucose-induced increases in HMW multimer production from human adipose explants correlated with changes in the two-dimensional electrophoresis profile of adiponectin isoforms. Collectively, these data suggest that adiponectin multimer composition is affected by changes in PTM in response to physiological factors.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

Development of New Structural Health Monitoring Techniques

During the past two decades, many researchers have developed methods for the detection of structural defects at the early stages to operate the aerospace vehicles safely and to reduce the operating costs. The Surface Response to Excitation (SuRE) method is one of these approaches developed at FIU to reduce the cost and size of the equipment. The SuRE method excites the surface at a series of frequencies and monitors the propagation characteristics of the generated waves. The amplitude of the waves reaching to any point on the surface varies with frequency; however, it remains consistent as long as the integrity and strain distribution on the part is consistent. These spectral characteristics change when cracks develop or the strain distribution changes. The SHM methods may be used for many applications, from the detection of loose screws to the monitoring of manufacturing operations. A scanning laser vibrometer was used in this study to investigate the characteristics of the spectral changes at different points on the parts. The study started with detecting a load on a plate and estimating its location. The modifications on the part with manufacturing operations were detected and the Part-Based Manufacturing Process Performance Monitoring (PbPPM) method was developed. Hardware was prepared to demonstrate the feasibility of the proposed methods in real time. Using low-cost piezoelectric elements and the non-contact scanning laser vibrometer successfully, the data was collected for the SuRE and PbPPM methods. Locational force, loose bolts and material loss could be easily detected by comparing the spectral characteristics of the arriving waves. On-line methods used fast computational methods for estimating the spectrum and detecting the changing operational conditions from sum of the squares of the variations. Neural networks classified the spectrums when the desktop – DSP combination was used. The results demonstrated the feasibility of the SuRE and PbPPM methods.

Development of New Structural Health Monitoring Techniques

During the past two decades, many researchers have developed methods for the detection of structural defects at the early stages to operate the aerospace vehicles safely and to reduce the operating costs. The Surface Response to Excitation (SuRE) method is one of these approaches developed at FIU to reduce the cost and size of the equipment. The SuRE method excites the surface at a series of frequencies and monitors the propagation characteristics of the generated waves. The amplitude of the waves reaching to any point on the surface varies with frequency; however, it remains consistent as long as the integrity and strain distribution on the part is consistent. These spectral characteristics change when cracks develop or the strain distribution changes. The SHM methods may be used for many applications, from the detection of loose screws to the monitoring of manufacturing operations. A scanning laser vibrometer was used in this study to investigate the characteristics of the spectral changes at different points on the parts. The study started with detecting a load on a plate and estimating its location. The modifications on the part with manufacturing operations were detected and the Part-Based Manufacturing Process Performance Monitoring (PbPPM) method was developed. Hardware was prepared to demonstrate the feasibility of the proposed methods in real time. Using low-cost piezoelectric elements and the non-contact scanning laser vibrometer successfully, the data was collected for the SuRE and PbPPM methods. Locational force, loose bolts and material loss could be easily detected by comparing the spectral characteristics of the arriving waves. On-line methods used fast computational methods for estimating the spectrum and detecting the changing operational conditions from sum of the squares of the variations. Neural networks classified the spectrums when the desktop – DSP combination was used. The results demonstrated the feasibility of the SuRE and PbPPM methods.

Adapting prospective structural analysis to strengthen sustainable management and capacity building in community-based natural resource management contexts

Local communities collectively managing common pool resources can play an important role in sustainable management, but they often lack the skills and context-specific tools required for such management. The complex dynamics of social-ecological systems (SES), the need for management capacities, and communities’ limited empowerment and participation skills present challenges for community-based natural resource management (CBNRM) strategies. We analyzed the applicability of prospective structural analysis (PSA), a strategic foresight tool, to support decision making and to foster sustainable management and capacity building in CBNRM contexts and the modifications necessary to use the tool in such contexts. By testing PSA in three SES in Colombia, Mexico, and Argentina, we gathered information regarding the potential of this tool and its adaptation requirements. The results suggest that the tool can be adapted to these contexts and contribute to fostering sustainable management and capacity building. It helped identify the systems’ dynamics, thus increasing the communities’ knowledge about their SES and informing the decision-making process. Additionally, it drove a learning process that both fostered empowerment and built participation skills. The process demanded both time and effort, and required external monitoring and facilitation, but community members could be trained to master it. Thus, we suggest that the PSA technique has the potential to strengthen CBNRM and that other initiatives could use it, but they must be aware of these requirements.

Platinum–tin/carbon catalysts for ethanol oxidation: Influence of Sn content on the electroactivity and structural characteristics

Carbon-supported Pt–Sn catalysts commonly contain Pt–Sn alloy and/or Pt–Sn bimetallic systems (Sn oxides). Nevertheless, the origin of the promotion effect due to the presence of Sn in the Pt–Sn/C catalyst towards ethanol oxidation in acid media is still under debate and some contradictions. Herein, a series of Ptx–Sny/C catalysts with different atomic ratios are synthesized by a deposition process using formic acid as the reducing agent. Catalysts structure and chemical compositions are investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) and their relationship with catalytic behavior towards ethanol electro-oxidation was established. Geometric structural changes are producing by highest Sn content (Pt1–Sn1/C) promoted the interaction of Pt and Sn forming a solid solution of Pt–Sn alloy phase, whereas, the intermediate and lowest Sn content (Pt2–Sn1/C and Pt3–Sn1/C, respectively) promoted the electronic structure modifications of Pt by Sn addition without the formation of a solid solution. The amount of Sn added affects the physical and chemical characteristics of the bimetallic catalysts as well as reducing the amount of Pt in the catalyst composition and maintaining the electrocatalytic activities at the anode. However, the influence of the Sn oxidation state in Pt–Sn/C catalysts surfaces and the alloy formation between Pt and Sn as well as with the atomic ratio on their catalytic activity towards ethanol oxidation appears minimal. Similar methodologies applied for synthesis of Ptx–Sny/C catalysts with a small change show differences with the results obtained, thus highlighting the importance of the conditions of the preparation method.

Exploring first-year academic achievement through structural equation modelling

The purpose of this research was to develop and test a multicausal model of the individual characteristics associated with academic success in first-year Australian university students. This model comprised the constructs of: previous academic performance, achievement motivation, self-regulatory learning strategies, and personality traits, with end-of-semester grades the dependent variable of interest. The study involved the distribution of a questionnaire, which assessed motivation, self-regulatory learning strategies and personality traits, to 1193 students at the start of their first year at university. Students' academic records were accessed at the end of their first year of study to ascertain their first and second semester grades. This study established that previous high academic performance, use of self-regulatory learning strategies, and being introverted and agreeable, were indicators of academic success in the first semester of university study. Achievement motivation and the personality trait of conscientiousness were indirectly related to first semester grades, through the influence they had on the students' use of self-regulatory learning strategies. First semester grades were predictive of second semester grades. This research provides valuable information for both educators and students about the factors intrinsic to the individual that are associated with successful performance in the first year at university.